Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,008,176 A→G 46.8% G282G (GGT→GGC)  hybO ← hydrogenase 2, small subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,008,1760AG46.8% 3.7 / 69.1 79G282G (GGT→GGC) hybOhydrogenase 2, small subunit
Reads supporting (aligned to +/- strand):  ref base A (28/14);  new base G (16/21);  total (44/35)
Fisher's exact test for biased strand distribution p-value = 4.37e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.66e-01

ATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGCC  >  minE/2008123‑2008238
                                                     |                                                              
aTACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAg                                                 >  1:829701/1‑69 (MQ=255)
aTACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAg                                                 >  1:2654566/1‑69 (MQ=255)
aTACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAg                                                 >  1:2728930/1‑69 (MQ=255)
aTACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAg                                                 >  1:178155/1‑69 (MQ=255)
aTACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAg                                                 >  1:3036704/1‑69 (MQ=255)
  aCCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGaa                                               >  1:2235682/1‑69 (MQ=255)
  aCCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGaa                                               >  1:1312827/1‑69 (MQ=255)
                   cATAGCAAGGGTGACCAATCGCCACCGGCCACACACGGCCAACATCGCAGAATTGCAGCGTTGAGCAGt                              >  1:1010087/1‑69 (MQ=255)
                   cATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAg                               >  1:695100/1‑68 (MQ=255)
                   cATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGt                              >  1:1187183/1‑69 (MQ=255)
                   cATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGt                              >  1:1202002/1‑69 (MQ=255)
                   cATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGt                              >  1:2315981/1‑69 (MQ=255)
                   cATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGt                              >  1:501106/1‑69 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCa                                                          >  1:1526307/1‑39 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAAc                                                        >  1:2303704/1‑41 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAg                                  >  1:1008856/1‑63 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTg                            >  1:1616056/1‑69 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTg                            >  1:510252/1‑69 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTg                            >  1:2912498/1‑69 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTg                            >  1:2815480/1‑69 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTg                            >  1:2333969/1‑69 (MQ=255)
                     tAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGAAGCGTTGAGCAGTTg                            >  1:3374013/1‑69 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:936828/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:417362/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:750589/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:2321604/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:245906/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:71245/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:564284/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:553167/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:300390/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:3035658/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:3076335/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:2195631/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:1494723/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:1550249/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGc                           >  1:168711/1‑68 (MQ=255)
                       gCACGGGTGACCAATCGCTACCGGCCACACGCCGCCAAAATCGCAGAATTGCAg                                         >  1:1489042/1‑54 (MQ=37)
                             gTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGt                    >  1:2031978/1‑69 (MQ=255)
                             gTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGt                    >  1:1190554/1‑69 (MQ=255)
                              tGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGtt                   <  1:3257520/69‑1 (MQ=255)
                              tGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGtt                   >  1:523274/1‑69 (MQ=255)
                              tGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGtt                   >  1:2203855/1‑69 (MQ=255)
                              tGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGtt                   <  1:1709206/69‑1 (MQ=255)
                              tGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGtt                   >  1:874605/1‑69 (MQ=255)
                                  cAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTg               >  1:299444/1‑69 (MQ=255)
                                     tCGCCACCGTCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:299828/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTTAGCAGTTGCCGTAAGTTTCTGGcc            <  1:391241/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:1827134/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:211452/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:506863/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:1653375/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:1557087/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:3065798/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:1290936/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:2551444/69‑1 (MQ=255)
                                     tCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGCTTCTGGcc            <  1:2783121/69‑1 (MQ=255)
                                       gCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGcc            <  1:44915/67‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTTCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:755111/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1320940/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1303024/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1267886/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:878809/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:761152/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:772213/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1134344/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1560257/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:3208749/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:3123875/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:3108044/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1576528/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1641657/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1644430/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:2849950/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:1835991/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:2513632/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:2503476/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:2371110/69‑1 (MQ=255)
                                               ccACACGCCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGcc  <  1:2340056/69‑1 (MQ=255)
                                                     |                                                              
ATACCTTCTTCGTTACAGCCATAGCAAGGGTGACCAATCGCCACCGGCCACACACCGCCAACATCGCAGAATTGCAGCGTTGAGCAGTTGCCGTAAGTTTCTGGCCCTTTACAGCC  >  minE/2008123‑2008238

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A